• Reactome

  • Referenced in 24 articles [sw14952]
  • visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems...
  • KEGGgraph

  • Referenced in 8 articles [sw06934]
  • KEGG), constructing manually curated pathway maps that represent current knowledge on biological networks in graph ... knowledge there is currently no software package to parse and analyze KEGG pathways with graph...
  • WikiPathways

  • Referenced in 1 article [sw29362]
  • WikiPathways: capturing the full diversity of pathway knowledge. WikiPathways (http://www.wikipathways.org) is an open, collaborative ... capturing and disseminating models of biological pathways for data visualization and analysis. Since our last...
  • Cellnoptr

  • Referenced in 5 articles [sw15114]
  • uses information on signaling pathways encoded as a Prior Knowledge Network, and trains it against...
  • RelEx

  • Referenced in 7 articles [sw35376]
  • regulatory pathways, signal cascades, metabolic processes or disease models requires knowledge on individual relations like...
  • STRING

  • Referenced in 34 articles [sw23938]
  • networks, with increased coverage and integration. Complete knowledge of all direct and indirect interactions between ... from raw data repositories to highly formalized pathway databases. For many applications, a global view...
  • pathClass

  • Referenced in 1 article [sw18854]
  • package pathClass: Classification using biological pathways as prior knowledge. pathClass is a collection of classification...
  • CellNOpt

  • Referenced in 2 articles [sw19834]
  • uses information on signaling pathways encoded as a Prior Knowledge Network, and trains it against...
  • SPINE

  • Referenced in 6 articles [sw29309]
  • protein effects and reconstruct signaling and regulatory pathways. Overall, we are able to infer ... high agreement with current biological knowledge. Availability: The algorithm and data are available...
  • TRANSPATH

  • Referenced in 7 articles [sw08272]
  • metabolic pathways. As one of the earliest pathway databases ever created, it has grown since ... integral part of the BIOBASE Knowledge Library (BKL)/ PROTEOME Database, but can also be obtained...
  • BioPath

  • Referenced in 4 articles [sw07462]
  • well-known Boehringer poster and the Biochemical Pathways atlas. These networks are very complex ... grow fast by the steady progress of knowledge in life sciences...
  • BioKEEN

  • Referenced in 3 articles [sw34085]
  • BioKEEN (Biological KnowlEdge EmbeddiNgs) and PyKEEN (Python KnowlEdge EmbeddiNgs) to facilitate their easy use through ... which we used a novel biological pathway mapping resource to predict links that represent pathway...
  • SNPs3D

  • Referenced in 5 articles [sw30035]
  • other data, such as expression profiles, pathway context, mouse knockout information and papers. Gene-gene ... combination of SNP impact analysis, a knowledge based network of gene relationships and candidate genes ... information, and so develop models of gene-pathway-disease interaction...
  • BioLattice

  • Referenced in 1 article [sw17687]
  • expression clusters with biomedical ontologies and/or biological pathways. However, this approach evaluates only one cluster ... experimental context. External knowledge resources such as Gene Ontology trees and pathway graphs...
  • BaCelLo

  • Referenced in 9 articles [sw17174]
  • balanced subcellular localization predictor. Motivation. The knowledge of the subcellular localization of a protein ... five classes of subcellular localization (secretory pathway, cytoplasm, nucleus, mitochondrion and chloroplast...
  • ReactomeFIViz

  • Referenced in 1 article [sw25625]
  • challenging task for biologists. Projecting data onto pathway and network contexts is a powerful ... seemingly scattered large data sets and assist knowledge discovery related to cancer and other complex ... functional interaction network combined with human curated pathways derived from Reactome and other pathway databases...
  • XGR

  • Referenced in 0 articles [sw15613]
  • range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes...
  • GeneWays

  • Referenced in 4 articles [sw23128]
  • extracting, analyzing, visualizing, and integrating molecular pathway data. The immense growth in the volume ... processing, information visualization, and generation of specialized knowledge bases for molecular biology. GeneWays...
  • iMPT-FRAKEL

  • Referenced in 0 articles [sw39602]
  • participate in. Compounds and 12 metabolic pathway types were retrieved from KEGG. Each compound ... limited prior knowledge of compounds but gives satisfying performance for recognizing metabolic pathways of compounds...
  • dmGWAS

  • Referenced in 3 articles [sw29291]
  • GWAS association data with that from prior-knowledge databases and proteome studies has recently gained ... value genes in GWAS datasets. Compared with pathway-based approaches, this method introduces flexibility...